Once you have the world and zones set up as services, you can start and stop them from the service manager.  Or you can use the command line.
NET START/STOP "service name"
see 
net /? for more options/info
so eqemu_stop.bat
	Code:
	net stop "zone_7995"
net stop "zone_7996"
net stop "zone_7997"
net stop "zone_7998"
net stop "zone_7999"
net stop "world"
 and eqemu_start.bat
	Code:
	net start "world"
net start "zone_7995"
net start "zone_7996"
net start "zone_7997"
net start "zone_7998"
net start "zone_7999"
 
And while the exact procedure may differ some this can be done on NT4.0 2k XP and 2003